Information on EC 1.1.1.387 - L-serine 3-dehydrogenase (NAD+)

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The expected taxonomic range for this enzyme is: Pseudomonas aeruginosa

EC NUMBER
COMMENTARY hide
1.1.1.387
-
RECOMMENDED NAME
GeneOntology No.
L-serine 3-dehydrogenase (NAD+)
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2-aminomalonate semialdehyde = 2-aminoacetaldehyde + CO2
show the reaction diagram
L-serine + NAD+ = 2-aminoacetaldehyde + CO2 + NADH + H+
show the reaction diagram
L-serine + NAD+ = 2-aminomalonate semialdehyde + NADH + H+
show the reaction diagram
SYSTEMATIC NAME
IUBMB Comments
L-serine:NAD+ 3-oxidoreductase
The enzyme, purified from the bacterium Pseudomonas aeruginosa, also shows activity with L-threonine (cf. EC 1.1.1.103, L-threonine 3-dehydrogenase). The enzyme has only very low activity with NADP+ [cf. EC 1.1.1.276, serine 3-dehydrogenase (NADP+)].
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
the enzyme might be involved in serine/threonine degradation. Since growth experiments with various nitrogen and carbon sources (including L-serine) reveal no difference between the Pseudomonas aeruginosa wild-type and PA0743 deletion strains, it is suggested hat this organism might contain other (complementing) serine dehydrogenases
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-glycerate + NAD+
?
show the reaction diagram
-
-
-
?
DL-threonine + NAD+
?
show the reaction diagram
-
-
-
?
L-serine + NAD+
?
show the reaction diagram
methyl 2,2-dimethyl-3-hydroxypropionate + NAD+
?
show the reaction diagram
-
-
-
?
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
L-serine + NAD+
?
show the reaction diagram
Q9I5I6
the enzyme might be involved in serine/threonine degradation. Since growth experiments with various nitrogen and carbon sources (including L-serine) reveal no difference between the Pseudomonas aeruginosa wild-type and PA0743 deletion strains, it is suggested hat this organism might contain other (complementing) serine dehydrogenases
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NAD+
the enzyme can also use NADP+ as a cofactor for the oxidation of L-serine, but this activity is significantly lower than that with NAD+ (4–6%)
NADP+
the enzyme can also use NADP+ as a cofactor for the oxidation of L-serine, but this activity is significantly lower than that with NAD+ (4–6%)
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
10.8
D-glycerate
pH 11.0, 37°C, wild-type enzyme
2.4
DL-threonine
pH 11.0, 37°C, wild-type enzyme
2.5 - 12.3
L-serine
17.4
methyl 2,2-dimethyl-3-hydroxypropionate
pH 11.0, 37°C, wild-type enzyme
-
3.4
NAD+
pH 11.0, 37°C, wild-type enzyme
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5.8
D-glycerate
Pseudomonas aeruginosa
Q9I5I6
pH 11.0, 37°C, wild-type enzyme
9.6
DL-threonine
Pseudomonas aeruginosa
Q9I5I6
pH 11.0, 37°C, wild-type enzyme
0.4 - 10.4
L-serine
11.6
methyl 2,2-dimethyl-3-hydroxypropionate
Pseudomonas aeruginosa
Q9I5I6
pH 11.0, 37°C, wild-type enzyme
-
1.6
NAD+
Pseudomonas aeruginosa
Q9I5I6
pH 11.0, 37°C, wild-type enzyme
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.3
D-glycerate
Pseudomonas aeruginosa
Q9I5I6
pH 11.0, 37°C, wild-type enzyme
521
4
DL-threonine
Pseudomonas aeruginosa
Q9I5I6
pH 11.0, 37°C, wild-type enzyme
9158
0.04 - 4
L-serine
95
0.7
methyl 2,2-dimethyl-3-hydroxypropionate
Pseudomonas aeruginosa
Q9I5I6
pH 11.0, 37°C, wild-type enzyme
202157
0.5
NAD+
Pseudomonas aeruginosa
Q9I5I6
pH 11.0, 37°C, wild-type enzyme
7
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
two crystal structures of the enzyme are solved at 2.2-2.3 A resolution and reveal an N-terminal Rossmann fold domain connected by a long alpha-helix to the C-terminal all-alpha-domain. The apostructure shows the presence of additional density modeled as HEPES bound in the interdomain cleft close to the predicted catalytic Lys171, revealing the molecular details of the enzyme substrate-binding site. The structure of the enzyme-NAD complex demonstrates that the opposite side of the enzyme active site accommodates the cofactor, which is also bound near Lys171. Crystals of the enzyme are grown at 21C by the hanging drop vapor diffusion method with 0.002 ml of protein sample mixed with an equal volume of the reservoir buffer. The crystals of the wild-type enzyme grew after 1 week in the presence of 4 M ammonium acetate and 0.1 M sodium acetate (pH 5.4). The crystals of the complex of the enzyme with NAD+ are obtained by soaking the crystals in 10 mM NAD+. For diffraction studies, the crystals are stabilized with the crystallization buffer supplemented with 12% ethylene glycol as a cryoprotectant and flash frozen in liquid nitrogen
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
overexpressed in Escherichia coli
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D247A
inactive protein
K171A
inactive protein
K246A
inactive protein
N175A
mutant enzyme with very low activity
S122A
mutant enzyme with very low activity
T96A
mutant enzyme with very low activity
W214A
inactive protein
Y219A
mutant enzyme with very low activity